CyTOF Workflow (CATALYST)

Use when working with CATALYST for mass-cytometry or flow-cytometry analysis in R/Bioconductor, including preprocessing with prepData, normCytof, assignPrelim, estCutoffs, applyCutoffs, computeSpillma

1 shared topic • 3 shared operations

stLearn — spatial transcriptomics analysis in Python integrating gene expression with tissue morphology. Provides SME (spatial morphological gene expression) normalization, spatial clustering, spatial

1 shared topic • 3 shared operations

ConsensusClusterPlus — R/Bioconductor package for determining cluster count and membership by stability evidence in unsupervised analysis, implementing the Monti et al. (2003) consensus clustering alg

1 shared topic • 2 shared operations

Giotto Suite — R toolkit for spatial multi-omics analysis at all scales and resolutions. Processes data from Visium, MERFISH, Xenium, CosMx, Slide-seq, CODEX, Stereo-seq, and other spatial technologie

1 shared topic • 2 shared operations

Scanpy — scalable Python toolkit for analyzing single-cell gene expression data built on AnnData. Provides preprocessing (QC, normalization, feature selection, dimensionality reduction), clustering (L

1 shared topic • 2 shared operations